idr (version 1.3)

idr-package: Irreproducible discovery rate

Description

This package estimates the reproducibility of observations on a pair of replicate rank lists. It consists of three components: (1) plotting the correspondence curve to visualize reproducibility, (2) quantifying reproducibility using a copula mixture model and estimating the posterior probability for each obsrvation to be irreproducible (local irreproducible discovery rate), and (3) ranking and selecting observations by their irreproducibility.

Details

Package:	idr
Type:	Package
Version:	1.2
Date:	2012-10-26
Updates:	Improve the convergence of est.IDR (2014-08-15)
License:	GPL-2
LazyLoad:	yes

The main functions are est.IDR(), get.correspondence() and select.IDR(). est.IDR estimates the copula mixture model and the posterior probability for each observation to be irreproducible. get.correspondence generates the values for plotting the correspondence curve. select.IDR ranks obervations by their reproducibility and reports the number of observations passing the specified IDR thresholds.

References

Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.

Examples

# NOT RUN {
data("simu.idr")
x <- cbind(-simu.idr$x, -simu.idr$y)

mu <- 2.6
sigma <- 1.3
rho <- 0.8
p <- 0.7

idr.out <- est.IDR(x, mu, sigma, rho, p, eps=0.001, max.ite=20)

names(idr.out)
# }